rino 0.1.0 → 0.2.0

data/ext/src/e_util.h

@@ -1,61 +0,0 @@
-/*
- * International Union of Pure and Applied Chemistry (IUPAC)
- * International Chemical Identifier (InChI)
- * Version 1
- * Software version 1.00
- * April 13, 2005
- * Developed at NIST
- */
-
-#ifndef __UTIL_H__
-#define __UTIL_H__
-
-/* BILLY 8/6/04 */
-#ifndef INCHI_ALL_CPP
-#ifdef __cplusplus
-extern "C" {
-#endif
-#endif
-
-int   e_extract_ChargeRadical( char *elname, int *pnRadical, int *pnCharge );
-int   e_normalize_name( char* name );
-
-int   e_mystrncpy(char *target,const char *source,unsigned maxlen);
-char *e_LtrimRtrim( char *p, int* nLen );
-void  e_remove_trailing_spaces( char* p );
-void  e_remove_one_lf( char* p);
-int   e_is_element_a_metal( char szEl[] );
-
-AT_NUMB *e_is_in_the_list( AT_NUMB *pathAtom, AT_NUMB nNextAtom, int nPathLen );
-S_SHORT *e_is_in_the_slist( S_SHORT *pathAtom, S_SHORT nNextAtom, int nPathLen );
-void     e_SplitTime( unsigned long ulTotalTime, int *hours, int *minutes, int *seconds, int *mseconds );
-
-/* allocator */
-#ifndef e_inchi_malloc
-void *e_inchi_malloc(size_t c);
-#endif
-#ifndef e_inchi_calloc
-void *e_inchi_calloc(size_t c, size_t n);
-#endif
-#ifndef e_inchi_free
-void e_inchi_free(void *p);
-#endif
-
-
-extern char e_gsMissing[];
-extern char e_gsEmpty[];
-extern char e_gsSpace[];
-extern char e_gsEqual[];
-/* format string for SDF_LBL_VAL(L,V): %s%s%s%s (four strings) */
-#define SDF_LBL_VAL(L,V)  ((L)&&(L)[0])?e_gsSpace:e_gsEmpty, ((L)&&(L)[0])?L:e_gsEmpty, ((L)&&(L)[0])? (((V)&&(V)[0])?e_gsEqual:e_gsSpace):e_gsEmpty, ((V)&&(V)[0])?V:((L)&&(L)[0])?e_gsMissing:e_gsEmpty
-
-
-/* BILLY 8/6/04 */
-#ifndef INCHI_ALL_CPP
-#ifdef __cplusplus
-}
-#endif
-#endif
-
-#endif /* __UTIL_H__*/
-

data/ext/src/ichilnct.c

@@ -1,286 +0,0 @@
-/*
- * International Union of Pure and Applied Chemistry (IUPAC)
- * International Chemical Identifier (InChI)
- * Version 1
- * Software version 1.00
- * April 13, 2005
- * Developed at NIST
- */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <limits.h>
-#include <math.h>
-#include <float.h>
-#include <string.h>
-#include <ctype.h>
-
-/* for use in the InChI library */
-
-#include "mode.h"
-#include "inchi_api.h"
-#include "util.h"
-#include "ichierr.h"
-#include "ichicomp.h"
-
-#define my_fgetsTab       l_my_fgetsTab
-#define my_fgetsTab1      l_my_fgetsTab1
-#define my_fgets          l_my_fgets
-#define str_fgetc         l_str_fgetc
-#define str_fgets         l_str_fgets
-#define str_fgetsTab      l_str_fgetsTab
-
-#define INChIToInchi_Atom l_INChIToInchi_Atom
-
-int INChIToInchi_Input( INCHI_FILE *inp_molfile, inchi_Input *orig_at_data, int bMergeAllInputStructures,
-                       int bDoNotAddH, INPUT_TYPE nInputType,
-                       char *pSdfLabel, char *pSdfValue, long *lSdfId, INCHI_MODE *pInpAtomFlags,
-                       int *err, char *pStrErr );
-
-/* This contains executable code. Included in lReadAux.c, e_ReadINCH.c, ReadINCH.c,  */
-#include "aux2atom.h"
-
-extern int bLibInchiSemaphore;
-/*****************************************************************************************************/
-EXPIMP_TEMPLATE INCHI_API int INCHI_DECL Get_inchi_Input_FromAuxInfo(
-                        char *szInchiAuxInfo, int bDoNotAddH, InchiInpData *pInchiInp )
-{
-    INCHI_FILE inp;
-    int num_at, nRet = inchi_Ret_OKAY, err = 0;
-    INCHI_MODE bChiral = 0;
-    /* the input string may contain the following line: "Structure NNN. HHH=VVV" */
-    long         lNumber;                   /* structure number NNN from the input */
-    char         szHeader[MAX_SDF_HEADER];  /* stucture label header HHH from the input */
-    char         szLabel[MAX_SDF_VALUE];    /* stucture label VVV from the input */
-    if ( bLibInchiSemaphore ) {  /* does not work properly under sufficient stress */
-        return inchi_Ret_BUSY;
-    }
-    bLibInchiSemaphore = 1;
-
-    if ( pInchiInp && pInchiInp->pInp ) {
-        /* clear output fields */
-        inchi_Input *pInp      = pInchiInp->pInp;
-        char        *szOptions = pInp->szOptions;
-        memset( pInchiInp, 0, sizeof(*pInchiInp) );
-        memset( pInp,      0, sizeof(*pInp) );
-        pInp->szOptions = szOptions;
-        pInchiInp->pInp = pInp;
-    } else {
-        bLibInchiSemaphore = 0;
-        return inchi_Ret_ERROR;
-    }
-    szHeader[0]     = '\0';
-    szLabel[0]      = '\0';
-    lNumber         = 0;
-    /* prepare input string pointers */
-    inp.pStr             = szInchiAuxInfo;
-    inp.nUsedLength      = strlen(szInchiAuxInfo);
-    inp.nAllocatedLength = inp.nUsedLength+1;
-    inp.nPtr             = 0;
-
-    num_at = INChIToInchi_Input( &inp, pInchiInp->pInp, 1, bDoNotAddH, INPUT_INCHI_PLAIN,
-                       szHeader, szLabel, &lNumber, &bChiral,
-                       &err, pInchiInp->szErrMsg );
-    pInchiInp->bChiral = bChiral;
-    if ( num_at <= 0 ) {
-        if ( 10 < err && err < 20 ) {
-            nRet = inchi_Ret_EOF;
-        } else
-        if ( err == 9 ) {
-            nRet = inchi_Ret_ERROR; /*  sdfile bypassed to $$$$ */
-        } else
-        if ( err && err < 30 ) {
-            nRet = inchi_Ret_FATAL;
-        } else
-        if ( 98 == err ) {
-            nRet =  inchi_Ret_WARNING; /* empty AuxInfo */
-        } else
-        if ( err ) {
-            nRet =  inchi_Ret_ERROR;
-        } else
-        if ( pInchiInp->szErrMsg[0] ) {
-            nRet = inchi_Ret_WARNING;
-        }
-    }
-    if ( nRet != inchi_Ret_OKAY && nRet != inchi_Ret_WARNING ) {
-        Free_inchi_Input( pInchiInp->pInp );
-        pInchiInp->bChiral = 0;
-    }
-    bLibInchiSemaphore = 0;
-    return nRet;
-}
-/*****************************************************************************************************/
-EXPIMP_TEMPLATE INCHI_API void INCHI_DECL Free_inchi_Input( inchi_Input *pInp )
-{
-    FreeInchi_Atom( &pInp->atom );
-    FreeInchi_Stereo0D ( &pInp->stereo0D );
-    pInp->num_atoms = 0;
-    pInp->num_stereo0D = 0;
-}
-
-
-/*#endif*/ /* INCHI_MAIN */
-
-#ifndef INCHI_LIBRARY
-#error "INCHI_LIBRARY MUST be defined here"
-#endif
-
-
-/**********************************************************************************/
-int INChIToInchi_Input( INCHI_FILE *inp_molfile, inchi_Input *orig_at_data, int bMergeAllInputStructures,
-                       int bDoNotAddH, INPUT_TYPE nInputType,
-                       char *pSdfLabel, char *pSdfValue, long *lSdfId, INCHI_MODE *pInpAtomFlags,
-                       int *err, char *pStrErr )
-{
-    /* inp_ATOM       *at = NULL; */
-    int             num_dimensions_new;
-    int             num_inp_bonds_new;
-    int             num_inp_atoms_new;
-    int             num_inp_0D_new;
-    inchi_Atom     *at_new     = NULL;
-    inchi_Atom     *at_old     = NULL;
-    inchi_Stereo0D *stereo0D_new = NULL;
-    inchi_Stereo0D *stereo0D_old = NULL;
-    int             nNumAtoms  = 0, nNumStereo0D = 0;
-    MOL_COORD      *szCoordNew = NULL;
-    MOL_COORD      *szCoordOld = NULL;
-    int            i, j;
-
-    if ( pStrErr ) {
-        pStrErr[0] = '\0';
-    }
-
-    /*FreeOrigAtData( orig_at_data );*/
-    if ( lSdfId )
-        *lSdfId = 0;
-    do {
-        
-        at_old       = orig_at_data? orig_at_data->atom      : NULL; /*  save pointer to the previous allocation */
-        stereo0D_old = orig_at_data? orig_at_data->stereo0D  : NULL;
-        szCoordOld = NULL;
-        num_inp_atoms_new =
-            INChIToInchi_Atom( inp_molfile, orig_at_data? &stereo0D_new:NULL, &num_inp_0D_new,
-                          bDoNotAddH, nInputType, orig_at_data? &at_new:NULL, MAX_ATOMS,
-                          &num_dimensions_new, &num_inp_bonds_new,
-                          pSdfLabel, pSdfValue, lSdfId, pInpAtomFlags, err, pStrErr );
-        if ( num_inp_atoms_new <= 0 && !*err ) {
-            MOLFILE_ERR_SET (*err, 0, "Empty structure");
-            *err = 98;
-        } else
-        if ( orig_at_data && !num_inp_atoms_new && 10 < *err && *err < 20 && orig_at_data->num_atoms > 0 && bMergeAllInputStructures ) {
-            *err = 0; /* end of file */
-            break;
-        } else
-        if ( num_inp_atoms_new > 0 && orig_at_data ) {
-            /*  merge pOrigDataTmp + orig_at_data => pOrigDataTmp; */
-            nNumAtoms    = num_inp_atoms_new + orig_at_data->num_atoms;
-            nNumStereo0D = num_inp_0D_new    + orig_at_data->num_stereo0D;
-            if ( nNumAtoms >= MAX_ATOMS ) {
-                MOLFILE_ERR_SET (*err, 0, "Too many atoms");
-                *err = 70;
-                orig_at_data->num_atoms = -1;
-            } else
-            if ( !at_old ) {
-                /* the first structure */
-                orig_at_data->atom         = at_new;            at_new            = NULL;
-                orig_at_data->num_atoms    = num_inp_atoms_new; num_inp_atoms_new = 0;
-                orig_at_data->stereo0D     = stereo0D_new;      stereo0D_new      = NULL;
-                orig_at_data->num_stereo0D = num_inp_0D_new;    num_inp_0D_new    = 0;
-            } else
-            if ( orig_at_data->atom = CreateInchi_Atom( nNumAtoms ) ) {
-                /*  switch at_new <--> orig_at_data->at; */
-                if ( orig_at_data->num_atoms ) {
-                    memcpy( orig_at_data->atom, at_old, orig_at_data->num_atoms * sizeof(orig_at_data->atom[0]) );
-                    /*  adjust numbering in the newly read structure */
-                    for ( i = 0; i < num_inp_atoms_new; i ++ ) {
-                        for ( j = 0; j < at_new[i].num_bonds; j ++ ) {
-                            at_new[i].neighbor[j] += orig_at_data->num_atoms;
-                        }
-                    }
-                }
-                FreeInchi_Atom( &at_old );
-                /*  copy newly read structure */
-                memcpy( orig_at_data->atom + orig_at_data->num_atoms,
-                        at_new,
-                        num_inp_atoms_new * sizeof(orig_at_data->atom[0]) );
-                /*  copy newly read 0D stereo */
-                if ( num_inp_0D_new > 0 && stereo0D_new ) {
-                    if ( orig_at_data->stereo0D = CreateInchi_Stereo0D( nNumStereo0D ) ) {
-                        memcpy( orig_at_data->stereo0D, stereo0D_old, orig_at_data->num_stereo0D * sizeof(orig_at_data->stereo0D[0]) );
-                        /*  adjust numbering in the newly read structure */
-                        for ( i = 0; i < num_inp_0D_new; i ++ ) {
-                            if ( stereo0D_new[i].central_atom >= 0 ) {
-                                stereo0D_new[i].central_atom += orig_at_data->num_atoms;
-                            }
-                            for ( j = 0; j < 4; j ++ ) {
-                                stereo0D_new[i].neighbor[j] += orig_at_data->num_atoms;
-                            }
-                        }
-                        FreeInchi_Stereo0D( &stereo0D_old );
-                        memcpy( orig_at_data->stereo0D+orig_at_data->num_stereo0D,
-                                stereo0D_new,
-                                num_inp_0D_new * sizeof(orig_at_data->stereo0D[0]) );
-                    } else {
-                        num_inp_0D_new = 0;
-                        MOLFILE_ERR_SET (*err, 0, "Out of RAM");
-                        *err = -1;
-                    }
-                } else {
-                    num_inp_0D_new = 0;
-                }
-                /* update lengths */
-                orig_at_data->num_atoms    += num_inp_atoms_new;
-                orig_at_data->num_stereo0D += num_inp_0D_new;
-            } else {
-                MOLFILE_ERR_SET (*err, 0, "Out of RAM");
-                *err = -1;
-            }
-        } else
-        if ( num_inp_atoms_new > 0 ) {
-            nNumAtoms += num_inp_atoms_new;
-        }
-        FreeInchi_Atom( &at_new );
-        num_inp_atoms_new = 0;
-        FreeInchi_Stereo0D( &stereo0D_new );
-        num_inp_0D_new = 0;
-
-    } while ( !*err && bMergeAllInputStructures );
-    /*
-    if ( !*err ) {
-        orig_at_data->num_components =
-            MarkDisconnectedComponents( orig_at_data );
-        if ( orig_at_data->num_components == 0 ) {
-            MOLFILE_ERR_SET (*err, 0, "No components found");
-            *err = 99;
-        }
-        if ( orig_at_data->num_components < 0 ) {
-            MOLFILE_ERR_SET (*err, 0, "Too many components");
-            *err = 99;
-        }
-    }
-    */
-    if ( szCoordNew ) {
-        inchi_free( szCoordNew );
-    }
-    if ( at_new ) {
-        inchi_free( at_new );
-    }
-    /*
-    if ( !*err ) {
-        if ( ReconcileAllCmlBondParities( orig_at_data->atom, orig_at_data->num_atoms ) ) {
-            MOLFILE_ERR_SET (*err, 0, "Cannot reconcile stereobond parities");
-            if (!orig_at_data->num_atoms) {
-                *err = 1;
-            }
-        }
-    }
-    */
-    if ( *err ) {
-        FreeInchi_Input( orig_at_data );
-    }
-    if ( *err && !(10 < *err && *err < 20) && pStrErr && !pStrErr[0] ) {
-        MOLFILE_ERR_SET (*err, 0, "Unknown error");  /*   <BRKPT> */
-    }
-    return orig_at_data? orig_at_data->num_atoms : nNumAtoms;
-}
-

data/ext/src/inchi_api.h

@@ -1,670 +0,0 @@
-/*
- * International Union of Pure and Applied Chemistry (IUPAC)
- * International Chemical Identifier (InChI)
- * Version 1
- * Software version 1.00
- * April 13, 2005
- * Developed at NIST
- */
-
-#ifndef __INHCH_API_H__
-#define __INHCH_API_H__
-
-/* radical definitions */
-typedef enum tagINCHIRadical {
-   INCHI_RADICAL_NONE    = 0,
-   INCHI_RADICAL_SINGLET = 1,
-   INCHI_RADICAL_DOUBLET = 2,
-   INCHI_RADICAL_TRIPLET = 3
-} inchi_Radical;
-
-/* bond type definitions */
-typedef enum tagINCHIBondType {
-   INCHI_BOND_TYPE_NONE    =  0,
-   INCHI_BOND_TYPE_SINGLE  =  1,
-   INCHI_BOND_TYPE_DOUBLE  =  2,
-   INCHI_BOND_TYPE_TRIPLE  =  3,
-   INCHI_BOND_TYPE_ALTERN  =  4
-} inchi_BondType;
-/* 2D stereo definitions */
-typedef enum tagINCHIBondStereo2D {
-   /* stereocenter-related; positive: the sharp end points to this atom  */
-   INCHI_BOND_STEREO_NONE           =  0,
-   INCHI_BOND_STEREO_SINGLE_1UP     =  1,
-   INCHI_BOND_STEREO_SINGLE_1EITHER =  4,
-   INCHI_BOND_STEREO_SINGLE_1DOWN   =  6,
-   /* stereocenter-related; negative: the sharp end points to the opposite atom  */
-   INCHI_BOND_STEREO_SINGLE_2UP     = -1,
-   INCHI_BOND_STEREO_SINGLE_2EITHER = -4,
-   INCHI_BOND_STEREO_SINGLE_2DOWN   = -6,
-   /* stereobond-related */
-   INCHI_BOND_STEREO_DOUBLE_EITHER  =  3 /* unknown stereobond geometry */
-} inchi_BondStereo2D;
-
-/*************************************************************************
- * Notes on using INCHI_BOND_STEREO_SINGLE_*  from inchi_BondStereo2D    *
- *                                                                       *
- * These stereo markings are used by InChI to characterize a stereogenic *
- * atom if and only if all neighbors of this atom have same z-coordinate *
- * as this atom (that is, in case of 2D fragment).                       *
- * The only exception is INCHI_BOND_STEREO_SINGLE_?EITHER marking which  *
- * always assigns to the atom an "unknown" parity (u).                   *
- *                                                                       *
- * Note that the -NEWPS InChI option changes 2D stereo interpretation:   *
- * only bonds that have sharp end pointing to the stereogenic atom are   *
- * considered as being out of plane and only sharp ends of               *
- * INCHI_BOND_STEREO_SINGLE_?EITHER bonds are considered to determine    *
- * whether the stereochemistry is unknown.                               *
- *************************************************************************/
-
-/* sizes definitions */
-#define MAXVAL                   20 /* max number of bonds per atom                 */
-#define ATOM_EL_LEN               6 /* length of ASCIIZ element symbol field        */
-#define NUM_H_ISOTOPES            3 /* number of hydrogen isotopes: protium, D, T   */
-#define ISOTOPIC_SHIFT_FLAG   10000 /* add to isotopic mass if isotopic_mass =      */
-                                    /* (isotopic mass - average atomic mass)        */
-#define ISOTOPIC_SHIFT_MAX      100 /* max abs(isotopic mass - average atomic mass) */
-
-#ifndef INCHI_US_CHAR_DEF
-typedef signed char   S_CHAR;
-typedef unsigned char U_CHAR;
-#define INCHI_US_CHAR_DEF
-#endif
-
-#ifndef INCHI_US_SHORT_DEF
-typedef signed short   S_SHORT;
-typedef unsigned short U_SHORT;
-#define INCHI_US_SHORT_DEF
-#endif
-
-typedef  S_SHORT AT_NUM;          /* atom number; starts from 0 */
-
-/*************************************************
- *
- *
- *  A T O M S   a n d   C O N N E C T I V I T Y
- *
- *
- *************************************************/
-
-typedef struct tagInchiAtom {
-    /* atom coordinates */
-    double x;
-    double y;
-    double z;
-    /* connectivity */
-    AT_NUM  neighbor[MAXVAL];     /* adjacency list: ordering numbers of */
-                                  /*            the adjacent atoms, >= 0 */
-    S_CHAR  bond_type[MAXVAL];    /* inchi_BondType */
-    /* 2D stereo */
-    S_CHAR  bond_stereo[MAXVAL];  /* inchi_BondStereo2D; negative if the */
-                                  /* sharp end points to opposite atom */
-    /* other atom properties */
-    char    elname[ATOM_EL_LEN];  /* zero-terminated chemical element name:*/
-                                  /* "H", "Si", etc. */
-    AT_NUM  num_bonds;            /* number of neighbors, bond types and bond*/
-                                  /* stereo in the adjacency list */
-    S_CHAR  num_iso_H[NUM_H_ISOTOPES+1]; /* implicit hydrogen atoms */
-                                  /* [0]: number of implicit non-isotopic H
-                                       (exception: num_iso_H[0]=-1 means INCHI
-                                       adds implicit H automatically),
-                                     [1]: number of implicit isotopic 1H (protium),
-                                     [2]: number of implicit 2H (deuterium),
-                                     [3]: number of implicit 3H (tritium) */
-    AT_NUM  isotopic_mass;        /* 0 => non-isotopic; isotopic mass or  */
-                                  /* ISOTOPIC_SHIFT_FLAG + mass - (average atomic mass) */
-    S_CHAR  radical;              /* inchi_Radical */
-    S_CHAR  charge;               /* positive or negative; 0 => no charge */
-}inchi_Atom;
-
-/*******************************************************************
- * Notes: 1. Atom ordering numbers (i, k, and atom[i].neighbor[j] below)
- *           start from zero; max. ordering number is (num_atoms-1).
- *        2. inchi_Atom atom[i] is connected to the atom[atom[i].neighbor[j]]
- *           by a bond that has type atom[i].bond_type[j] and 2D stereo type
- *           atom[i].bond_stereo[j] (in case of no stereo
- *           atom[i].bond_stereo[j] = INCHI_BOND_STEREO_NONE)
- *           Index j is in the range 0 <= j <= (atom[i].num_bonds-1)
- *        3. Any connection (represented by atom[i].neighbor[j],
- *           atom[i].bond_type[j], and atom[i].bond_stereo[j])
- *           should be present in one or both adjacency list:
- *             if k = atom[i].neighbor[j] then i may or may not be present in
- *           atom[k].neighbor[] list. For example, the adjacency lists may be
- *           populated with only such neighbors that atom[i].neighbor[j] < i
- *           All elements of an adjacency list must be different, that is,
- *           a bond must be specified in an adjacency list only once.
- *        4. in Molfiles usually
- *           (number of implicit H) = Valence - SUM(bond_type[])
- *        5. Seemingly illogical order of the inchi_Atom members was
- *           chosen in an attempt to avoid alignment problems when
- *           accessing inchi_Atom from unrelated to C programming
- *           languages such as Visual Basic.
- *******************************************************************/
-
-/*******************************************************************
-    0D Stereo Parity and Type definitions
- *******************************************************************
-            Note:
-            =====
-            o Below #A is the ordering number of atom A, starting from 0
-            o See parity values corresponding to 'o', 'e', and 'u' in
-              inchi_StereoParity0D definition below)
-
-           =============================================
-            stereogenic bond >A=B< or cumulene >A=C=C=B<
-           =============================================
-
-                                 neighbor[4]  : {#X,#A,#B,#Y} in this order
-     X                           central_atom : NO_ATOM
-      \            X      Y      type         : INCHI_StereoType_DoubleBond
-       A==B         \    /
-           \         A==B
-            Y
-
-    parity= 'e'    parity= 'o'   unknown parity = 'u'
-
-    Limitations:
-    ============
-    o Atoms A and B in cumulenes MUST be connected by a chain of double bonds;
-      atoms A and B in a stereogenic 'double bond' may be connected by a double,
-      single, or alternating bond.
-    o One atom may belong to up to 3 stereogenic bonds (i.g. in a fused
-      aromatic structure).
-    o Multiple stereogenic bonds incident to any given atom should
-      either all except possibly one have (possibly different) defined
-      parities ('o' or 'e') or should all have an unknown parity 'u'.
-
-      Note on parities of alternating stereobonds
-      ===========================================
-                                                     D--E
-      In large rings  (see Fig. 1, all              //   \\
-      atoms are C) all alternating bonds         B--C      F--G
-      are treated as stereogenic.              //              \\
-      To avoid "undefined" bond parities      A                  H
-      for bonds BC, DE, FG, HI, JK, LM, AN     \               /
-      it is recommended to mark them with       N==M       J==I
-      parities.                                     \     /
-                                                      L==K    Fig. 1
-      Such a marking will make
-      the stereochemical layer unambiguous
-      and it will be different from the          B--C      F--G
-      stereochemical layer of the second       //   \\   //    \\
-      structure (Fig. 2).                     A      D--E        H
-                                               \               /
-                                                N==M       J==I
-      By default, double and alternating            \     /
-      bonds in 8-member and greater rings             L==K    Fig. 2
-      are treated by InChI as stereogenic.
-
-
-           =============================================
-            tetrahedral atom
-           =============================================
-
-   4 neighbors
-
-            X                    neighbor[4] : {#W, #X, #Y, #Z}
-            |                    central_atom: #A
-         W--A--Y                 type        : INCHI_StereoType_Tetrahedral
-            |
-            Z
-   parity: if (X,Y,Z) are clockwize when seen from W then parity is 'e' otherwise 'o'
-   Example (see AXYZW above): if W is above the plane XYZ then parity = 'e'
-
-   3 neighbors
-
-              Y          Y       neighbor[4] : {#A, #X, #Y, #Z}
-             /          /        central_atom: #A
-         X--A  (e.g. O=S   )     type        : INCHI_StereoType_Tetrahedral
-             \          \
-              Z          Z
-
-   parity: if (X,Y,Z) are clockwize when seen from A then parity is 'e',
-                                                          otherwise 'o'
-   unknown parity = 'u'
-   Example (see AXYZ above): if A is above the plane XYZ then parity = 'e'
-   This approach may be used also in case of an implicit H attached to A.
-
-           =============================================
-            allene
-           =============================================
-
-       X       Y                 neighbor[4]  : {#X,#A,#B,#Y}
-        \     /                  central_atom : #C
-         A=C=B                   type         : INCHI_StereoType_Allene
-
-                                      Y      X
-                                      |      |
-     when seen from A along A=C=B:  X-A    Y-A
-
-                          parity:   'e'    'o'
-
-   parity: if A, B, Y are clockwise when seen from X then parity is 'e',
-                                                          otherwise 'o'
-   unknown parity = 'u'
-   Example (see XACBY above): if X on the diagram is above the plane ABY
-                                                      then parity is 'o'
-
-   Limitations
-   ===========
-   o Atoms A and B in allenes MUST be connected by a chain of double bonds;
-
-   ==============================================
-   Note. Correspondence to CML 0D stereo parities
-   ==============================================
-   a list of 4 atoms corresponds to CML atomRefs4
-
-   tetrahedral atom
-   ================
-       CML atomParity > 0 <=> INCHI_PARITY_EVEN
-       CML atomParity < 0 <=> INCHI_PARITY_ODD
-
-                                    | 1   1   1   1  |  where xW is x-coordinate of
-                                    | xW  xX  xY  xZ |  atom W, etc. (xyz is a
-       CML atomParity = determinant | yW  yX  yY  yZ |  'right-handed' Cartesian
-                                    | zW  zX  xY  zZ |  coordinate system)
-
-   allene (not yet defined in CML)
-   ===============================
-   the parity corresponds to the sign of the following determinant
-   in exactly same way as for tetrahedral atoms:
-
-       | 1   1   1   1  |  where bonds and neighbor[4] array are
-       | xX  xA  xB  xY |  same as defined above for allenes
-       | yX  yA  yB  yY |  Obviously, the parity is same for
-       | zX  zA  xB  zY |  {#X,#A,#B,#Y} and {#Y,#B,#A,#X}
-                           because of the even number of column permutations.
-
-   stereogenic double bond and (not yet defined in CML) cumulenes
-   ==============================================================
-       CML 'C' (cis)      <=> INCHI_PARITY_ODD
-       CML 'T' (trans)    <=> INCHI_PARITY_EVEN
-
-
-   How InChI uses 0D parities
-   ==========================
-
-   1. 0D parities are used if all atom coordinates are zeroes.
-
-   In addition to that:
-
-   2. 0D parities are used for Stereobonds, Allenes, or Cumulenes if:
-
-   2a. A bond to the end-atom is shorter than MIN_BOND_LEN=0.000001
-   2b. A ratio of two bond lengths to the end-atom is smaller than MIN_SINE=0.03
-   2c. In case of a linear fragment X-A=B end-atom A is treated as satisfying 2a-b
-
-       0D parities are used if 2a or 2b or 2c applies to one or both end-atoms.
-
-   3. 0D parities are used for Tetrahedral Atoms if at least one of 3a-c is true:
-
-   3a. One of bonds to the central atom is shorter than MIN_BOND_LEN=0.000001
-   3b. A ratio of two bond lengths to the central atom is smaller than MIN_SINE=0.03
-   3c. The four neighbors are almost in one plane or the central atom and
-       its only 3 explicit neighbors are almost in one plane
-
-   Notes on 0D parities and 'undefined' stereogenic elements
-   =========================================================
-
-   If 0D parity is to be used according to 1-3 but    CH3     CH3
-   has not been provided then the corresponding         \    /
-   stereogenic element is considered 'undefined'.        C=CH
-                                                        /
-   For example, if in the structure (Fig. 3)           H
-   the explicit H has been moved so that it                Fig. 3
-   has same coordinates as atom >C= (that is,
-   the length of the bond H-C became zero)
-   then the double bond is assigned 'undefined'       CH3      CH3
-   parity which by default is omitted from the          \     /
-   Identifier.                                           CH=CH
-
-   However, the structure on Fig. 4 will have double        Fig. 4
-   bond parity 'o' and its parity in the Identifier is (-).
-
-   Notes on 0D parities in structures containing metals
-   ====================================================
-   Since InChI disconnects bonds to metals the 0D parities upon the
-   disconnection may change in several different ways:
-
-   1) previously non-stereogenic bond may become stereogenic:
-
-         \     /                            \     /  
-          CH==CH          disconnection      CH==CH  
-           \ /               ======>                 
-            M                                  M     
-
-     before the disconnection:    after the disconnection:
-     atoms C have valence=5 and   the double bond may become
-     the double bond is not       stereogenic
-     recognized as stereogenic
-
-   2) previously stereogenic bond may become non-stereogenic:
-
-       M                           M(+)       
-        \    /                             / 
-         N==C      disconnection    (-)N==C  
-             \        ======>              \ 
-
-   3) Oddball structures, usually resulting from projecting 3D
-      structures on the plane, may contain fragment like that
-      depicted on Fig. 5:
-
-              M   A                      M   A   
-              |\ /   B                      /   B 
-              | X   /     disconnection    /   /  
-              |/ \ /         ======>      /   /   
-              C===C                      C===C    
-             Fig. 5
-     (X stands for bond intersection)
-    
-     A-C=C-B parity is              A-C=C-B parity is
-     trans (e)                      cis (o) or undefined
-     because the bond               because C valence = 3,
-     orientation is same            not 4.
-     as on Fig, 6 below:
-
-          A       M
-           \     /     Removal of M from the structure
-            C===C      on Fig. 5 changes the geometry from trans
-           /     \     to cis. 
-          M'      B    Removal of M and M' from the structure
-          Fig. 6       on Fig. 6 does not change the A-C=C-B
-                       geometry: it is trans.
-
-   To resolve the problem InChI API accepts the second parity
-   corresponding to the metal-disconnected structure.
-   To store both bond parities use left shift by 3 bits:
-
-   inchi_Stereo0D::parity = ParityOfConnected | (ParityOfDisconnected<<3)
-
-   In case when only disconnected structure parity exists set
-   ParityOfConnected = INCHI_PARITY_UNDEFINED.
-   This is the only case when INCHI_PARITY_UNDEFINED parity
-   may be fed to the InChI.
-
-   In cases when the bond parity in a disconnected structure exists and
-   differs from the parity in the connected structure the atoms A and B
-   should be non-metals.
-
-****************************************************************************/
-
-#define NO_ATOM          (-1) /* non-existent (central) atom */
-
-/* 0D parity types */
-typedef enum tagINCHIStereoType0D {
-   INCHI_StereoType_None        = 0,
-   INCHI_StereoType_DoubleBond  = 1,
-   INCHI_StereoType_Tetrahedral = 2,
-   INCHI_StereoType_Allene      = 3
-} inchi_StereoType0D;
-
-/* 0D parities */
-typedef enum tagINCHIStereoParity0D {
-   INCHI_PARITY_NONE      = 0,
-   INCHI_PARITY_ODD       = 1,  /* 'o' */
-   INCHI_PARITY_EVEN      = 2,  /* 'e' */
-   INCHI_PARITY_UNKNOWN   = 3,  /* 'u' */
-   INCHI_PARITY_UNDEFINED = 4   /* '?' -- should not be used; however, see Note above */
-} inchi_StereoParity0D;
-
-
-/*************************************************
- *
- *
- *  0D - S T E R E O  (if no coordinates given)
- *
- *
- *************************************************/
-
-
-typedef struct tagINCHIStereo0D {
-    AT_NUM  neighbor[4];    /* 4 atoms always */
-    AT_NUM  central_atom;   /* central tetrahedral atom or a central */
-                            /* atom of allene; otherwise NO_ATOM */
-    S_CHAR  type;           /* inchi_StereoType0D */
-    S_CHAR  parity;         /* inchi_StereoParity0D: may be a combination of two parities: */
-                            /* ParityOfConnected | (ParityOfDisconnected << 3), see Note above */
-}inchi_Stereo0D;
-
-/*************************************************
- *
- *
- *  I N C h I    D L L     I n p u t
- *
- *
- *************************************************/
-
-typedef struct tagINCHI_Input {
-    /* the caller is responsible for the data allocation and deallocation */
-    inchi_Atom     *atom;         /* array of num_atoms elements */
-    inchi_Stereo0D *stereo0D;     /* array of num_stereo0D 0D stereo elements or NULL */
-    char           *szOptions;    /* InChI options: space-delimited; each is preceded by */
-                                  /* '/' or '-' depending on OS and compiler */
-    AT_NUM          num_atoms;    /* number of atoms in the structure < 1024 */
-    AT_NUM          num_stereo0D; /* number of 0D stereo elements */
-}inchi_Input;
-
-/*************************************************
- *
- *
- *  I N C h I     D L L     O u t p u t
- *
- *
- *************************************************/
-
-typedef struct tagINCHI_Output {
-    /* zero-terminated C-strings allocated by GetINCHI() */
-    /* to deallocate all of them call FreeINCHI() (see below) */
-    char *szInChI;     /* InChI ASCIIZ string */
-    char *szAuxInfo;   /* Aux info ASCIIZ string */
-    char *szMessage;   /* Error/warning ASCIIZ message */
-    char *szLog;       /* log-file ASCIIZ string, contains a human-readable list */
-                       /* of recognized options and possibly an Error/warning message */
-} inchi_Output;
-
-/*************************************************
- *
- *
- *  I N C h I      D L L     I n t e r f a c e
- *
- *
- *************************************************/
-
-#if (defined( _WIN32 ) && defined( _MSC_VER ) && defined(INCHI_LINK_AS_DLL) )
-    /* Win32 & MS VC ++, compile and link as a DLL */
-    #ifdef _USRDLL
-        /* InChI library dll */
-        #define INCHI_API __declspec(dllexport)
-        #define EXPIMP_TEMPLATE
-        #define INCHI_DECL __stdcall
-     #else
-        /* calling the InChI dll program */
-        #define INCHI_API __declspec(dllimport)
-        #define EXPIMP_TEMPLATE extern
-        #define INCHI_DECL __stdcall
-     #endif
-#else
-    /* create a statically linked InChI library or link to an executable */
-    #define INCHI_API
-    #define EXPIMP_TEMPLATE
-    #define INCHI_DECL
-#endif
-
-/* GetINCHI(...) and Get_inchi_Input_FromAuxInfo(...) return values: */
-
-typedef enum tagRetValGetINCHI {
- 
-    inchi_Ret_SKIP    = -2, /* not used in InChI library */
-    inchi_Ret_EOF     = -1, /* no structural data has been provided */
-    inchi_Ret_OKAY    =  0, /* Success; no errors or warnings */
-    inchi_Ret_WARNING =  1, /* Success; warning(s) issued */
-    inchi_Ret_ERROR   =  2, /* Error: no InChI has been created */
-    inchi_Ret_FATAL   =  3, /* Severe error: no InChI has been created (typically, memory allocation failure) */
-    inchi_Ret_UNKNOWN =  4, /* Unknown program error */
-    inchi_Ret_BUSY    =  5  /* Previuos call to InChI has not returned yet */
-
-} RetValGetINCHI;
-
-/* to compile all InChI code as a C++ code #define INCHI_ALL_CPP */
-#ifndef INCHI_ALL_CPP
-#ifdef __cplusplus
-extern "C" {
-#endif
-#endif
-
-/* inchi_Input is created by the user; strings in inchi_Output are allocated and deallocated by InChI */
-/* inchi_Output does not need to be initilized out to zeroes; see FreeINCHI on how to deallocate it   */
-EXPIMP_TEMPLATE INCHI_API int INCHI_DECL GetINCHI( inchi_Input *inp, inchi_Output *out );
-
-/* FreeINCHI() should be called to deallocate char* pointers obtained from each GetINCHI() call */
-EXPIMP_TEMPLATE INCHI_API void INCHI_DECL FreeINCHI ( inchi_Output *out );
-
-/* helper: get string length */
-EXPIMP_TEMPLATE INCHI_API int INCHI_DECL GetStringLength( char *p );
-
-
-
-#ifndef INCHI_ALL_CPP
-#ifdef __cplusplus
-}
-#endif
-#endif
-
- /**********************************************************
-     Using inchi_Input::szOptions related to ChiralFlag
-  **********************************************************
-  Awailable options (use - instead of / for O.S. other than MS Windows):
-  
-      /SUCF            Use Chiral Flag
-      /ChiralFlagON    Set Chiral Flag
-      /ChiralFlagOFF   Set Not-Chiral Flag
-
-   The following table describes the effect of the options
-   ---------------------------------------------------------------
-   Options               Equivalent to    Chiral Flag Information
-                                          stored in AuxInfo
-   ---------------------------------------------------------------
-   /SUCF /ChiralFlagON    /SABS             Chiral Flag
-   /SUCF /ChiralFlagOFF   /SREL             Not-Chiral Flag 
-   /SUCF                  /SREL             none
-   /ChiralFlagON           none             Chiral Flag
-   /ChiralFlagOFF          none             Not-Chiral Flag
-
-  *************************************************************
-    Other options available in InChI Library (case insensitive)
-  *************************************************************
-    /SNon        Exclude stereo (Default: Include Absolute stereo)
-    /SRel        Relative stereo
-    /SRac        Racemic stereo
-
-    /SUU         Include omitted unknown/undefined stereo
-    /NEWPS       Narrow end of wedge points to stereocenter (default: both)
-    /RecMet      Include reconnected bond to metal results
-    /FixedH      Mobile H Perception Off (Default: On)
-    /AuxNone     Omit auxiliary information (default: Include)
-    /NoADP       Disable Aggressive Deprotonation (for testing only)
-    /Compress    Compressed output
-    /DoNotAddH   Overrides inchi_Atom::num_iso_H[0] == -1
-    /Wnumber     Set time-out per structure in seconds; W0 means unlimited
-                 In InChI library the default value is unlimited
-    /OutputSDF   Output SDfile instead of InChI
-    /WarnOnEmptyStructure Warn and produce empty InChI for empty structure
-
-    Empty InChI format:   InChI=1//
-                          AuxInfo=1//
-*/
-
-
-/*****************************************************************
- *
- *
- *   C o n v e r s i o n:   InChI  AuxInfo string => inchi_Input
- *
- *
- *****************************************************************/
-
-#ifndef STR_ERR_LEN
-#define STR_ERR_LEN     256
-#endif
-
-typedef struct tagInchiInpData {
-    inchi_Input *pInp;    /* a pointer to pInp that has all items 0 or NULL */
-    int          bChiral; /* 1 => the structure was marked as chiral, 2=> not chiral, 0=> not marked */
-    char         szErrMsg[STR_ERR_LEN];
-} InchiInpData;
-
-/* to compile all InChI code as a C++ code #define INCHI_ALL_CPP */
-#ifndef INCHI_ALL_CPP
-#ifdef __cplusplus
-extern "C" {
-#endif
-#endif
-
-/*  Input
-    -----
-    szInchiAuxInfo: contains ASCIIZ string of InChI output for a single
-                   structure or only the AuxInfo line
-    bDoNotAddH:    if 0 then InChI will be allowed to add implicit H
-    pInchiInp:     should have a valid pointer pInchiInp->pInp to an empty 
-                   (all members = 0) inchi_Input structure 
-
-    Output
-    ------
-    pInchiInp:     The following members of pInp may be filled during the call:
-                   atom, num_atoms, stereo0D, num_stereo0D
-    Return value:  see RetValGetINCHI
-*/
-EXPIMP_TEMPLATE INCHI_API int INCHI_DECL Get_inchi_Input_FromAuxInfo
-             ( char *szInchiAuxInfo, int bDoNotAddH, InchiInpData *pInchiInp );
-
-/*
-    To deallocate and write zeroes into the changed members of pInchiInp->pInp call
-    Free_inchi_Input( inchi_Input *pInp )
-*/
-EXPIMP_TEMPLATE INCHI_API void INCHI_DECL Free_inchi_Input( inchi_Input *pInp );
-
-#ifndef INCHI_ALL_CPP
-#ifdef __cplusplus
-}
-#endif
-#endif
-
-
-/* Annotated List of -Exports for libinchi.dll produced by dumpbin (Win32):
-
- ordinal hint RVA      name
---------------------------------- C calling conventions, compatible with gcc under Win32
-                                  (see inchi_dll.c and vc6_libinchi.def for details)
-       1    0 0004D800 FreeINCHI
-       2    1 0004D840 Free_inchi_Input
-       3    2 0004D7F0 GetINCHI
-       4    3 0004D810 GetStringLength
-       5    4 0004D820 Get_inchi_Input_FromAuxInfo
---------------------------------- __stdcall calling conventions, compatible with MS VB 6
-                                  (as defined in this file and used in INCHI_MAIN.exe)
-       6    5 0004BD30 _FreeINCHI@4
-       7    6 0001D7C0 _Free_inchi_Input@4
-       8    7 0004BD80 _GetINCHI@8
-       9    8 0004D7D0 _GetStringLength@4
-      10    9 0001D620 _Get_inchi_Input_FromAuxInfo@12
-
-------------------- end of the Annotated list-----------------------
-
-=======================================================================
-============= prototypes for C calling conventions: ===================
-=======================================================================
-int  GetINCHI( inchi_Input *inp, inchi_Output *out );
-void FreeINCHI( inchi_Output *out );
-int  GetStringLength( char *p );
-int  Get_inchi_Input_FromAuxInfo
-     ( char *szInchiAuxInfo, int bDoNotAddH, InchiInpData *pInchiInp );
-void Free_inchi_Input( inchi_Input *pInp );
-=======================================================================
-
-
-
-*/
-
-/* Currently there is no callback function for aborting, progress, etc. */
-
-#endif /* __INHCH_API_H__ */